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Old 11-04-2009, 01:07 AM   #1
Magnus
Junior Member
 
Location: Uppsala, Sweden

Join Date: Nov 2009
Posts: 5
Default Memory problems with MosaikAligner 1.0.1307 (removed -km and -pm)

Hi

There was an option in "old" MosaikAligner to load the keys-file, and/or positions-file into the memory by using "-km" and "-pm" from a reference jump database. I was never able to load both into memory due to lack of sufficient RAM, (loaded just the keys-file). This features are now removed in "new" MosaikAligner, and I am not able to aligne with my new jump-database.

Are there any tricks besides upgrading the hardware to get around this problem?

Error message:
Code:
------------------------------------------------------------------------------
MosaikAligner 1.0.1307                                              2009-10-14
Michael Stromberg & Wan-Ping Lee  Marth Lab, Boston College Biology Department
------------------------------------------------------------------------------

- Using the following alignment algorithm: all positions
- Using the following alignment mode: aligning reads to all possible locations
- Using a maximum mismatch threshold of 6
- Using a hash size of 15
- Aligning in colorspace (SOLiD)
- Using 4 processors
- Using an alignment candidate threshold of 25bp.
- Setting hash position threshold to 100
- Using a jump database for hashing. Storing keys & positions in memory.
- loading basespace reference sequences... finished.
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
Aborted
Server:
Linux 2.6.25-gentoo-r7 #1 SMP x86_64 Intel(R) Xeon(R) CPU E5440 @ 2.83GHz GenuineIntel GNU/Linux
cat /proc/meminfo gives "MemTotal: 16430836 kB"
cat /proc/cpuinfo gives "8 times Intel(R) Xeon(R) CPU E5440 @ 2.83GHz"
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-km, -pm, memory, mosaik, mosaikaligner

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